Thank you for your post.
stderr should not have excessive blank lines, and no similar issue has been reported. I do not know what would cause this issue, but I can assure you it is not normal.
My recommendation would be to stop FileMaker Server, move your database files from the Databases folder to the Desktop, uninstall FileMaker Server, remove the FileMaker Server folder, and reinstall. Once installed, move the database files from the Desktop to the FileMaker Server Databases folder.
If you notice any further oddities with the the stderr file, please let me know.
At the time the problem occurred I truncated stderr using the method I mentioned above and restarted the server machine. So far it has been running for 8 days and stderr is only 8KB and has not been growing. I'll post again if the problem re-occurs and I am keeping an eye on other servers to see if I spot the same problem.
I have had a similar situation occur. Ran out of disk space, had to force shut down everything. Made room by deleting some extraneous back up files related to an ERP upgrade. Everything running ok again but did an OmniSweep and saw that the FMS logs folder was over 30GBs. Can I simply delete the stderr log file? Will a new one be generated then?
Yes, you can delete the stderr.log file, but not while FileMaker Server is running. Be sure to not only stop FileMaker Server, but also any corresponding services. Then, delete stderr.log file, and reboot the server.